title: Increasing the mass accuracy of high-resolution LC-MS data using background ions: a case study on the LTQ-Orbitrap.
abstract: With the advent of a new generation of high-resolution mass spectrometers, the fields of proteomics and metabolomics have gained powerful new tools. In this paper, we demonstrate a novel computational method that improves the mass accuracy of the LTQ-Orbitrap mass spectrometer from an initial +/- 1-2 ppm, obtained by the standard software, to an absolute median of 0.21 ppm (SD 0.21 ppm). With the increased mass accuracy it becomes much easier to match mass chromatograms in replicates and different sample types, even if compounds are detected at very low intensities. The proposed method exploits the ubiquitous presence of background ions in LC-MS profiles for accurate alignment and internal mass calibration, making it applicable for all types of MS equipment. The accuracy of this approach will facilitate many downstream systems biology applications, including mass-based molecule identification, ab initio metabolic network reconstruction, and untargeted metabolomics in general.
authors.affiliation: Groningen Bioinformatics Centre, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Haren, The Netherlands.
authors.forename: Richard A
authors.initials: RA
authors.lastname: Scheltema
authors.forename: Anas
authors.initials: A
authors.lastname: Kamleh
authors.forename: David
authors.initials: D
authors.lastname: Wildridge
authors.forename: Charles
authors.initials: C
authors.lastname: Ebikeme
authors.forename: David G
authors.initials: DG
authors.lastname: Watson
authors.forename: Michael P
authors.initials: MP
authors.lastname: Barrett
authors.forename: Ritsert C
authors.initials: RC
authors.lastname: Jansen
authors.forename: Rainer
authors.initials: R
authors.lastname: Breitling
mesh_terms: D002853:Chromatography, Liquid / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D007477:Ions; D013058:Mass Spectrometry / Q000379:methods*; D055442:Metabolome; D055432:Metabolomics / Q000379:methods*; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012680:Sensitivity and Specificity; D012984:Software
chemical_list: D007477:Ions; D020543:Proteome